Strain identifier

BacDive ID: 24796

Type strain: Yes

Species: Orbus sasakiae

Strain Designation: C7

Strain history: J.-W. Bae C7.

NCBI tax ID(s): 1078475 (species)

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General

@ref: 21216

BacDive-ID: 24796

DSM-Number: 27928

keywords: 16S sequence, Bacteria, facultative anaerobe, Gram-negative, coccus-shaped

description: Orbus sasakiae C7 is a facultative anaerobe, Gram-negative, coccus-shaped bacterium that was isolated from gut of butterfly Sasakia charonda.

NCBI tax id

  • NCBI tax id: 1078475
  • Matching level: species

strain history

@refhistory
21216<- KACC <- J. Y. Kim et al., Kyung Hee Univ., Seoul, Republic of Korea
67770J.-W. Bae C7.

doi: 10.13145/bacdive24796.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Orbales
  • family: Orbaceae
  • genus: Orbus
  • species: Orbus sasakiae
  • full scientific name: Orbus sasakiae Kim et al. 2013

@ref: 21216

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Orbales

family: Orbaceae

genus: Orbus

species: Orbus sasakiae

full scientific name: Orbus sasakiae Kim et al. 2013

strain designation: C7

type strain: yes

Morphology

cell morphology

  • @ref: 30679
  • gram stain: negative
  • cell length: 0.75 µm
  • cell width: 0.75 µm
  • cell shape: coccus-shaped
  • motility: no

pigmentation

  • @ref: 30679
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21216
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21216positivegrowth20-25
30679positivegrowth04-37
30679positiveoptimum22.5psychrophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
30679positivegrowth06-10alkaliphile
30679positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30679
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
30679NaClpositivegrowth0-5 %
30679NaClpositiveoptimum1 %

observation

@refobservation
30679aggregates in clumps
67770quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3067917057cellobiose+carbon source
3067916947citrate+carbon source
3067923652dextrin+carbon source
3067915740formate+carbon source
3067928757fructose+carbon source
3067933984fucose+carbon source
3067928260galactose+carbon source
3067917234glucose+carbon source
3067917716lactose+carbon source
3067937684mannose+carbon source
3067928053melibiose+carbon source
3067937657methyl D-glucoside+carbon source
30679506227N-acetylglucosamine+carbon source
3067951850methyl pyruvate+carbon source
3067916634raffinose+carbon source
3067930031succinate+carbon source
3067917992sucrose+carbon source
3067926986threonine+carbon source
3067953423tween 40+carbon source
3067953426tween 80+carbon source
3067916704uridine+carbon source
3067917632nitrate+reduction
6836830849L-arabinose-fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole+

enzymes

@refvalueactivityec
30679acid phosphatase+3.1.3.2
30679alkaline phosphatase+3.1.3.1
30679catalase+1.11.1.6
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
21216+-------++-+-----++--

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
21216gut of butterfly Sasakia charondaSasakia charondaRepublic of KoreaKORAsia
67770Gut of the butterfly Sasakia charondaSasakia charondaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Arthropoda#Insecta
#Host Body-Site#Gastrointestinal tract#Stomach

taxonmaps

  • @ref: 69479
  • File name: preview.99_27146.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_84;96_13469;97_16396;98_20337;99_27146&stattab=map
  • Last taxonomy: Orbus
  • 16S sequence: JN561614
  • Sequence Identity:
  • Total samples: 302
  • soil counts: 5
  • aquatic counts: 8
  • animal counts: 284
  • plant counts: 5

Safety information

risk assessment

  • @ref: 21216
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21216
  • description: Orbus sasakiae strain C7 16S ribosomal RNA gene, partial sequence
  • accession: JN561614
  • length: 1301
  • database: ena
  • NCBI tax ID: 1078475

GC content

@refGC-contentmethod
3067932.1
6777032.1thermal denaturation, midpoint method (Tm)

External links

@ref: 21216

culture collection no.: DSM 27928, JCM 18050, KACC 16544

straininfo link

  • @ref: 88618
  • straininfo: 408369

literature

  • topic: Phylogeny
  • Pubmed-ID: 22941300
  • title: Orbus sasakiae sp. nov., a bacterium isolated from the gut of the butterfly Sasakia charonda, and emended description of the genus Orbus.
  • authors: Kim JY, Lee J, Shin NR, Yun JH, Whon TW, Kim MS, Jung MJ, Roh SW, Hyun DW, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.041871-0
  • year: 2012
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Butterflies/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification, Gastrointestinal Tract/*microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21216Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27928Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27928)
30679Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172701028776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
88618Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID408369.1